Hi, On Fri, Aug 8, 2008 at 3:12 PM, Vitaly Chaban <[EMAIL PROTECTED]> wrote: > No problem, Prasun. :) Just open conf.gro and see the last string > there. Divide the least number by 2 and type it in the grompp.mdp as > your new cutoff. >
This is a good way of turning gromacs into the well-known expensive random number generator! Unless there's a good reason why the box has the dimensions it should have and unless one knows what he/she's doing by changing rvdw, the rvdw shouldn't be modified in this way. The cut-off (shift/...) is an integral part of a force field. A force field is parameterized using (and thus to be used with) a specific combination of simulation parameters. Changing these at random will affect the integrity of the force field. On another note, when using pressure coupling, taking half the box size for rvdw may make the simulation fail pretty quickly if the box contracts (and we'll get another question on this list...). > > <The cut-off length is longer than half the shortest box vector or longer > <than the smallest box diagonal element. Increase the box size or decrease >>rvdw. > The answer of Justin was right on, set a larger distance between periodic images. If -d doesn't serve you well, because the solute is to small, set the box dimensions using the option '-box' :) Cheers, Tsjerk > -- > Vitaly V. Chaban > School of Chemistry > National University of Kharkiv > Svoboda sq., 4, Kharkiv 61077, Ukraine > email: [EMAIL PROTECTED] > skype: vvchaban > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
